Phantom Fairy
by Etcetera-Gal
Summary: Naruto's training trip with Jiraiya is cut short when there is an emergency in Konoha. Tsunade is in a coma, Danzo is Hokage, and Naruto is told he will be locked away. Having to escape from his own village, Naruto promises to be back one day and soon finds himself joining a certain guild in the land of Fiore. What path will he walk from here on out?


Disclaimer: I do not own Naruto or Fairy Tail

Summary: Naruto's training trip with Jiraiya is cut short when there is an emergency in Konoha. Tsunade is in a coma, Danzo is Hokage, and Naruto is told he will be locked away. Having to escape from his own village, Naruto promises to be back one day and soon finds himself joining a certain guild in the land of Fiore.

Chapter 1

Naruto sucked in a quick deep breathe, relishing the brief moment of a cool feeling in his lungs. It was way too hot to be anywhere but the shade but here he was trudging along after Jiraiya in a wide open field. They had only left Konoha 3 days ago and all of Naruto's enthusiasm for this "training trip", as Jiraiya called it, had dwindled away to almost nothing. So far, all they had done was walk. Naruto wanted to get strong and fulfil his promise to Sakura as soon as possible. He knew that 3 days wasn't that long but he was frustrated that all he'd done so far was torturous marching under the sun.

"Ne, Ero-sennin" Naruto piped up as he wiped some sweat from his brow. "When are we gonna start training? I need to get stronger if I want to bring Sasuke back to Konoha"

"Sheesh" Jiraiya stopped and looked back at his student from over his shoulder. He didn't like all this walking in the scorching heat either but he had to make sure they were out of the Akatsuki's sights. "We'll stop for camp tonight and start training there tomorrow. Day after we'll head out again" he explained, being as to the point as he could. This heat had really lowered his tolerance levels. He was tempted to just drop to the ground in the next patch of shade he could find. But they only had a short way to go before he was confident that they were outside of the Akatsuki's reach. Although, it would be far too optimistic to think it would stay that way for long. This training trip was going to be a pain in the ass. They'd have to constantly be on the move to stay ahead of any members of the Akatsuki who may be after Naruto.

As Jiraiya continued walking along his thoughts began to descend into darker territory. He was predicting the grim possibilities of the future, including a wide scope of probabilities. Just a few steps behind him, Naruto was also considering the future possibilities but his thought were more narrowed and focused on his wayward teammate. Naruto had promised Sakura to bring Sasuke back and he'd also made a promise to Sasuke himself that he would bring him back to Konoha even if it meant having to break every bone in his body and drag him back. But how long it would be before he could accomplish that, and what would happen afterwards was a worry he tried to keep at the back of his mind.

But neither of them, in any of their thoughts of possibilities, did they think of what would happen next. They had just started setting up camp that night when a shinobi bearing the Leaf symbol appeared. He looked worn and was out of breath, but wasted no time in telling them they had to head back to the village immediately. Naruto had leaped up from his seat on a withering log to protest, saying that they hadn't even started training yet. But as Jiraiya began demanding more information, the shinobi let loose some news which shocked him into silence.

"Lady Tsunade has fallen ill. She collapsed and no one can wake her up, it's like she's comatose. The council has demanded you return as quickly as possible" he told them in a firm and serious voice.

Naruto stood stock-still, wondering if he'd heard right. How could Tsunade, who had punched Jiraiya through a wall 3 days ago, be in a coma? It didn't make sense. Something had to be wrong here but who would lie about this? The wild pace of Naruto's thoughts came to a halt as Jiraiya barked an order to get his gear. He hurried about the camp site stuffing all his belongings into his backpack. He'd been so relieved to free himself of the pack's weight earlier when they had stopped to make camp, but now it seemed that he could not get it on his back fast enough. As soon as he was ready he looked over at Jiraiya who had just stuffed the last of his "research" books into his bag and slung the cloth sack over his shoulder. With barely even a glance around them, they took off and sped towards Konoha as fast as they could.

The muscles in Naruto's limbs ached, especially his legs. All that walking in the glaring sun had tired him out but the cool night air had given him a fresh feeling. It rejuvenated him and he felt no need to slow down or stop running. But what kept him charging forward was not this sense of revival. It was his thoughts of the Hokage and just what could possibly have caused her collapsing. If it was serious enough to warrant calling them back, in spite of the threat of the Akatsuki, then it must be bad.

What the hell was happening in Konoha?

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With the much faster pace, they shaved a day off their travel time and reached the village gates after 2 days. Naruto was out of breath but still keen on moving, wanting to go see Tsunade. Maybe she had woken up since and was now just fine. But as a shinobi escort appeared he instructed only Jiraiya to follow him and told Naruto that he was to follow the group of ANBU which had arrived shortly after he did. Of course, this struck him as odd, but this was no time to be asking question and wasting valuable time. Besides, his breath was coming and going in such great heaves that nobody here would understand a word he was saying. So he just quietly followed the ANBU and watched over his shoulder as Jiraiya followed his escort in another direction.

He was taken to a blank room with only a small square of a window letting in light. Naruto thought to himself that it almost felt like a prison cell as he sat down on one of only two chairs in the room. He had caught his breath a while ago but he still remained silent thanks to a growing knot of unease in his stomach. On their way here, the ANBU had walked closely and seemed have boxed him in. He had been given the distinct feeling that he had no choice in going with them or not. So for them to have led him to such a dismal place was starting to freak him out a bit. It only got worse as the ANBU filed out of the room, wordlessly closing the door behind them. Was this a prison cell after all?

No, Naruto had done nothing wrong so there'd be no reason to lock him up.

Logic worked its way into his brain and Naruto felt the tension in his body disperse and his shoulders slump. He was just worked up from the frantic dash back to the village. He needed to take a moment to breathe and calm down. He leaned forward in the chair, resting his forearms on his legs. He ignored the discomfort in his sore leg muscles and began to think over this entire mess. But he had no more luck making sense of it as he did on the way here. For now, he'd just have to wait for Jiraiya.

But as hours slipped by Naruto began to realise that something. The ANBU outside had brought in some food and water for him and he had jumped at the chance to ask questions. Problem was they were all met with silence. As a growing suspicion began tightening the knot in his stomach Naruto approached the door and carried out a test. The door was locked.

No communication between him and the ANBU? Food brought in on trays and left for him by the door? The door of a prison-like room locked tight?

Earlier, he had not been overreacting as he had told himself. He really is a prisoner.

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Meanwhile, Jiraiya was losing his patience. His escort had taken his sweet time leading him to Tsunade and no matter how many questions he asked along the way he was only given vague answers and had learned very little. It had been several hours since he had arrived back at the village gates and he had still yet to see the reason why he was here. At the moment, he was sitting on the edge of a seat in the waiting room. His tapping foot was a clear sign of his irritation but he had already tried barging into the room twice already. The first time he was stopped by the nurses who were saying that they needed the room clear of distractions. That had made him worry. It had been about 5 days ago when Tsunade initially collapsed and she still needed such attention? He had complied with the nurses at the time but as an hour slipped by without a word he attempted another entry. But his reason for failing that time had been a surprise he had not expected.

Homura, of the councillors, had intervened. He had abruptly announced himself as Jiraiya started exchanging words with the nurse. He had told him to be patient and let the doctors and nurses do their work. In exchange for obedience, Jiraiya gained some answers. Homura explained to him upon being questioned that Tsunade had been found by her secretary on the floor of her office, passed out. Shizune had immediately called for aid and Tsunade had been admitted to hospital soon after. They have yet to determine whether it is an issue of health or whether the Hokage had actually suffered an attack of some kind.

That had really been all he managed to learn from the councillor and Jiraiya's curiosity was hardly satisfied. But what bothered him the most was how everyone seemed to be handling the matter. First he had been escorted, [very slowly], by a shinobi who barely gave a straight answer to even one question. Then he'd been sat down in a waiting room for over an hour. And then one of the councillors had joined him. Who ever heard of a councillor standing around a waiting room, completely unfazed by knowing so little? Jiraiya was sure that Homura could use his authority to enter the Hokage's hospital, and he was the type to do it. So why was he just patiently standing there with a stone face. Could it be he was here just to keep Jiraiya in check?

Damn it, none of what was happening seemed to make sense.

"Jiraiya-sama" a voice interrupted his thoughts and his head whirled round towards the door. The nurse stood next to the open door and told him that it was alright to enter now. He rushed in, almost bumping into Homura as the old man also made his way into the Hokage's room.

"I'm afraid she still remains unresponsive but she is in no danger. Other than being comatose, we cannot detect anything wrong with her" the aged doctor stated as he watched Jiraiya approach the bed.

"It took you that long to come up with that?" Jiraiya snapped at him but only sent a glance in his direction. Most of his focus went to the form lying limp on the bed. Tsunade looked like she was sleeping and there really didn't seem to be any visible signs of something wrong. Her breathing was calm and regular, her complexion was the usual shade, and there was no pained expression on her face. Jiraiya almost breathed a sigh of relief but the mystery behind her condition still weighed heavy on his mood. He turned to Homura who was now standing a few steps away from the foot of the bed.

"What's being done to figure this out? You have to be running some kind of investigation" he asked, getting straight to business. And this time he wasn't going to put up with any round-a-bout answers. He glared up at Homura from beside Tsunade's bed, her limp hand clasped in his own.

"Of course there is an investigation" Homura replied tersely. "It is being headed by the Hokage replacement"

"Her replacement?!" Jiraiya repeated to make sure he had heard him right. "When did that happen?" Tsunade had only been out for a week and she was already replaced?

"Konoha is in no state to be without a leader, we had to appoint someone to take her place" Homura explained, seeing the need to justify his actions though not pleased about it. "As of now, he is only a stand in. But if Tsunade-sama should not wake, it may very well become a permanent position. However, Danzo-sama is up for the task"

"Danzo?! Are you kidding me?!" Jiraiya stood up straight and the tried glaring the man down. Crap just kept on piling up on more crap. How could this be happening? Did Danzo have something to do with all this?

"Where is he?" Jiraiya asked, calming himself. He had to speak to Danzo and work his way into the investigation. He knew Danzo had always been eyeing the Hokage seat and he was not happy with development. He would have to check things but carefully.

As he went about his own investigation, Jiraiya's thoughts were far from his student who was currently glaring fiercely at the very man Jiraiya was asking to see. By now, he was in chains and the ANBU stood silently behind him no doubt ready to plunge a kunai into his skin at a moment's notice. Naruto had to fight back the urge to jump up and start demanding answers. Danzo stared down at him with little emotion showing on his bandaged face. Even with such little expression, Naruto felt as though he was looking at a speck of dirt and it made him angry. He gritted his teeth to keep back the harsh words he felt rising in his throat.

"I find it astounding that you have been let to roam so freely before now" Danzo finally spoke. "It was only a matter of time before something like this occurred. The Akatsuki are far too much a threat to allow you to fall into their hands". At this point he was no longer looking at Naruto. As though he was not worth his attention, Danzo had taken some papers from the man behind him and began browsing the contents.

"What the hell is that all supposed to mean?!" Naruto finally shouted out, "Ero-sennin is gonna teach me to be stronger than them and we left to train to avoid bringing them here"

"A foolish tactic as you are no doubt easier to acquire beyond Konoha's walls" Danzo's reply was spoken in a flat voice as though he was stating the most obvious thing in the world. "The only way to foil whatever plans the Akatsuki have for the nine-tailed beast is by locking you away where no one can find you"

"Wha-?" he choked on his own question before he could even finish the first word. What did he just say? Something about locking him up...where no one could find him. That had to be a joke, right? But the stone cold face which he found himself staring at with mouth agape seemed dead serious.

"As the new Hokage, I have all the authority to do this" Danzo stated in a finalizing voice before turning and leaving the cell. The ANBU followed him out but most likely remained just outside the thick metal door. Naruto just stared after them in disbelief, it was rare for him to keep quiet but the shock had stolen his voice. And so, lost for words, Naruto just swallowed loudly and glared up at the door before him. He knew there was nothing he could do and he would just have to wait for Tsunade to wake up. She wouldn't let this happen and Jiraiya would wake her up soon. But the thought that Danzo would lock him away somewhere even the Hokage could not find was indeed worrying.

Not being known for patience, Naruto found himself doing the opposite of what he had decided to do several hours later. His legs were void of feeling from the awkward sitting position the chains forced him to stay in. His hands were busy at work trying to loosen his bindings but so far all he had done was cut up the skin on his wrists. The tiny window barely helped his sight as night had fallen and only dim moonlight leaked through. His stomach growled at him furiously and Naruto briefly stopped his fidgeting to glance at the tray of food near him. Only a short while ago had a shinobi brought it in and he guessed it meant he'd been here long enough that it was now dinner time. But in his stubborn ways, Naruto had refused to take a single bite from the food. The quick glance had weakened that resolve but he soon distracted himself into forgetting it by returning his attention back to the chained cuffs around his wrists. But soon he found himself distracted but something else; a noise outside the door. Were the ANBU coming back in?

He was sure he heard something but as he stares at the door nothing happens. Naruto lets his gaze fall to the floor and his head hang low. He was surprised by the feeling a disappointment that created a chill in his chest. Had he actually thought someone was there to help him? How stupid. But as he curses himself there is a loud click from the door and it slowly creaks open. Naruto looks up. Was it Danzo again?

"Naruto, about time I find you" Jiraiya struck a pose with a big grin on his face. It hadn't been easy sneaking through the facility avoiding detection while checking out each cell for his missing student.

"Ero-sen-" Naruto's shout was halted by a hand roughly covering his mouth. Jiraiya crouched down in front of him and held up a single finger before his mouth. A well known sign for quiet and Naruto nodded in response. Jiraiya moved his hand away and quickly moved around him to do away with the bindings.

"I don't know how he did it but I'm sure Danzo has something to do with Tsunade's condition" Jiraiya stated in a hushed voice which was accompanied by the clinking of chains. "Problem is; there's no evidence so I have to bust you out" Jiraiya's mouth was set in a firm line as he set the loose chains on the cold, stone floor. Naruto stood up and wrapped his sore wrists, smearing the blood. When he turned to look at his teacher he was unsure of what to make of the expression worn on the sennin's face. But before he could ask any questions, Jiraiya gestured for him to follow him and they carefully left the cell. They tied up the unconscious ANBU and gagged them so they could not send out an alarm upon awakening. After locking them up in the very cell which they had held Naruto, teacher and student silently make their way out of the facility. Naruto was almost caught several times as he lacked experience in stealth but with Jiraiya leading the way they made it out without being discovered. Once they were outside Naruto began asking questions in a quietened voice but when some prison guards on patrol passed by, forcing them to duck into a bush for cover, Jiraiya told him to hang on a little longer and he would explain once they were clear. A few minutes later the two were moving through the streets of Konoha, sticking to narrow alleys and places without light.

"Oi, Ero-sennin" Naruto spoke just above a whisper as they finished rounding a corner into an empty alley between two buildings. "Where are we going" Naruto glanced about him paranoid of getting caught. Jiraiya must have some plan but he himself was drawing a blank.

"Danzo may have sensors working for him so I'll wait 'til we're clear of the village to summon a Toad" Jiraiya replied without looking back, keeping his focus on their surroundings.

"And do what? You going after Danzo?" Naruto asked as he crouched down to get by a window unseen by the people inside.

"Are you stupid? That kind of strategy will get us nowhere and worse, it could Tsunade killed" Jiraiya hissed, finally coming to a stop near a stack of crates. He turned to look at Naruto and shrugged off the pack on his back before handing it to him. Naruto took one glance as he took it from the extended hand and immediately recognised it as his own. Jiraiya must have found his backpack when he was looking for him in the prison.

"We'll stick with our original plan" the Toad Sage told him grimly. His words confused Naruto as he couldn't recall just whatever plan he was talking about. But before the blonde could ask for a better answer there was a noise off to their right. Both shinobi spun their heads in that direction on high alert. As a shadowy figure appeared in the connecting street, Naruto pressed himself closer to the wall trying to melt into the shadows.

"He's not here" the stranger stated as another figure approached him.

"Keep looking. He couldn't have gotten far, he's just a genin" the new arrival said back and the two dispersed beyond the sight of the two crouched in the alleyway.

"Damn, they already know you're out" Jiraiya scowled, muttering under his breath more than actually speaking to Naruto. He hurriedly led the way through the streets, occasionally stopping to duck into a place to hide. Naruto was still in the dark about everything that had happened and was dying to know the answers to his questions but he kept his mouth shut for the sake of stealth. Even in this serious situation, Naruto couldn't help but make an inward remark about how this was probably the quietest he'd been in a long time. But his brief joking was forgotten as it began to feel like the walls were closing in. Almost every corner had someone to sneak around now and they were finding fewer available routes. Naruto even considered using the sewers like he did when he was a kid hiding from angry villagers. But as a sense of dread grew to chilling proportions there was a break in the dark night. Light streamed out from a newly opened door and the two shinobi had to duck behind the trees which lined the fenced off yard. They had jumped the fence to hide from one of their hunters but now there was someone walking their way from the house. Naruto carefully poked his head over the fence and ducked back down as he saw not just the one pursuer from before but three. Jiraiya had obviously seen this as well as he breathed out a curse. They were definitely in a bad spot.

They both turned their attention to the approaching figure who was heading directly for them. Since they came out of that house they were probably just a civilian. But once they see them crouching in the backyard in the middle of the night they will probably give away their position to the men on the other side of the fence.

Naruto had to focus to control his breathing but as seconds passed by at a painstakingly slow rate, the sound of his breathing seemed to flood his ears. His heart was pounding away and each beat sounded as loud as the bang of a drum. His attention was so focused on the dark yard before him that he almost gave himself away when a hand slapped down on the stone fence just above his head. He tilted his head back to look up, hoping not to see a face looking back down. Luckily all he could see were the tips of four fingers and he figured that whoever owned them was just leaning on the fence. But in that moment of panic he had forgotten about the approaching danger in the other direction.

"What are you doing?" Naruto almost choked on the air in his throat as his frantic eyes locked onto the person standing just a few steps away. His mind had just enough time to register the fact that this was a familiar face before he heard the shinobi from behind the fence speak up.

"Who's there? State your name" a gruff voice commanded. The newly arrived on the scene person briefly glanced down at the two shinobi crouched down by the fence and then flicked up to the three other shinobi who were clearly unaware of the former's presence.

"Nara. My name's Shikamaru Nara. Now will you tell me what you're doing?" Shikamaru stated and kept his gaze above the fence line. Naruto had sent him a pleading look and while he didn't know what it meant, he knew it was troublesome. Just what had he done this time?

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**Author's Note:** Yay! My first story has begun. Please send a review my way to tell me what you think. Oh, and as for the Fairy Tail part of the story, that's still to come but it will be soon.


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